Tracing Cell Aggregates

[denniris]

Hello,
   
I am trying to use ImageJ to trace my cell aggregates, and I was wondering
if there was a way for the program to automatically trace them. I currently use polygon selections to trace my cells but it is time consuming. Attached is an example and dead cells need to be excluded from the trace.

[ctrueden]

Hi Denniris,

> I am trying to use ImageJ to trace my cell aggregates, and I was
> wondering if there was a way for the program to automatically trace
> them.

As discussed on IRC [1], here is a macro that identifies your cell
aggregates as objects in the ROI manager:

  run("Find Edges");
  setAutoThreshold("Huang dark");
  run("Create Mask");
  run("Fill Holes");
  run("Analyze Particles...", "size=1000-Infinity add");
  close();

See also:
- http://imagej.net/Segmentation
- http://imagej.net/Macros
- http://imagej.net/Macros#The_recorder
- http://imagej.net/Using_the_Command_Launcher

Regards,
Curtis

[1]
http://code.imagej.net/chatlogs/fiji-devel?times=prefix&start-date=2015-02-13&start-time=1050&end-date=2015-02-13&end-time=1211


On Tue, Feb 10, 2015 at 1:34 AM, denniris <[hidden email]> wrote:

> Hello,
>
> I am trying to use ImageJ to trace my cell aggregates, and I was wondering
> if there was a way for the program to automatically trace them. I currently
> use polygon selections to trace my cells but it is time consuming. Attached
> is an example and dead cells need to be excluded from the trace.
> <http://imagej.1557.x6.nabble.com/file/n5011543/Test.jpg>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Tracing-Cell-Aggregates-tp5011543.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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